Putting these three terms into Google shows that there's some discussions already on GBATemp: "diskex iso wii"
It appears that you use "DiskEx -a -c" on a command line. That is probably the best topic to read since it comes up with results more than once on Google but it's sooooooooooo long.

So what do these tools actually do? Just let you compress data with a decent encoder? Resize (change the data rate, actually) images and sounds? Cut out extra junk like updates and support for other languages? I know that some optimizing tools for OS install discs will make multiple copies of the same file be reduced to just one copy with all the files pointing to the exact same real spot on the disc. However, I seriously doubt this last one would help on Wii games.

I've just been using GCMUtility for GC games. What they do is take out garbage data that is just there as filler to take up free space on the disc, and in the case of Wii games, they also remove updates.

Ah, so the system uses extra space for copy protection purposes (read: annoy copiers or measure timing ala Tages) or is it a limitation to the GC disc's format that the bootloaders totally bypass with images?